Dhananjay wrote:
Hello all,
I am running mdrun for a system of protein having 182 residues. (Before
going for MD, mdrun for EM and PR has been done as per the
instructions given in the online manual.)
After 3ns job is over, I calculated RMSD and it is about 0.6 nm. This
is too high.
In the mailing list, most of the search suggests that RMSD may be high
depends on the system.
One of the mails suggests to calculate RMSD domainwise. Hence I have
calculated it domainwise as the system consists of two domains. I found
that one of the domains has RMSD about 0.35 nm but the other domain is
still showing around 0.6 nm
please give more details,
amount of water,
force field,
ions
where does that starting structure come from
etc.
Is there something wrong in assigning the parameter ?
Please give me suggestions.........
Thanking you in advance.
The full mdrun paramitors are as follows:
title = xyz
cpp = /usr/bin/cpp
constraints = all-bonds
integrator = md
dt = 0.001 ; ps !
nsteps = 20000000 ; total 20 ns
nstcomm = 1
nstxout = 500
nstvout = 1000
nstfout = 0
nstlist = 10
nstlog = 10
nstenergy = 10
ns_type = grid
rlist = 0.9 ; nm
coulombtype = PME
rcoulomb = 0.9 ; nm
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in three groups
Tcoupl = berendsen
tau_t = 0.1 0.1
tc_grps = protein sol
ref_t = 300 300
; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
--
Dhananjay
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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